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comparison slopBed.xml @ 1:82aac94b06c3 draft

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author iuc
date Thu, 08 Jan 2015 14:25:51 -0500
parents b8348686a0b9
children 607c0576c6ab
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0:b8348686a0b9 1:82aac94b06c3
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[
9 bedtools slop 10 bedtools slop
10 $pct 11 $pct
11 $strand 12 $strand
12 -g $genome 13 -g $genome
13 -i $inputA 14 -i $inputA
14 #if $addition.addition_select == 'b': 15 #if $addition.addition_select == 'b':
15 -b $addition.b 16 -b $addition.b
16 #else: 17 #else:
17 -l $addition.l 18 -l $addition.l
18 -r $addition.r 19 -r $addition.r
19 #end if 20 #end if
20 $header 21 $header
21 22 > $output
22 &gt; $output 23 ]]>
23 </command> 24 </command>
24 <inputs> 25 <inputs>
25 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> 26 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
26 <expand macro="genome" /> 27 <expand macro="genome" />
27 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" label="Define -l and -r as a fraction of the feature’s length" help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" /> 28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
28 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Define -l and -r based on strand" help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> 29 label="Define -l and -r as a fraction of the feature’s length"
30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue=""
32 label="Define -l and -r based on strand"
33 help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
29 <expand macro="addition" /> 34 <expand macro="addition" />
30 <param name="header" type="boolean" checked="false" truevalue="-header" falsevalue="" label="Print the header from the input file prior to results." /> 35 <expand macro="print_header" />
31 </inputs> 36 </inputs>
32 <outputs> 37 <outputs>
33 <data format="bed" name="output" label=""/> 38 <data format="bed" name="output"/>
34 </outputs> 39 </outputs>
40 <tests>
41 <test>
42 <param name="inputA" value="a.bed" ftype="bed" />
43 <param name="genome" value="mm9_chr1.len" ftype="bed" />
44 <param name="addition_select" value="b" />
45 <param name="b" value="5" />
46 <output name="output" file="slopBed_result1.bed" ftype="bed" />
47 </test>
48 <test>
49 <param name="inputA" value="a.bed" ftype="bed" />
50 <param name="genome" value="mm9_chr1.len" ftype="bed" />
51 <param name="addition_select" value="lr" />
52 <param name="l" value="2" />
53 <param name="r" value="3" />
54 <output name="output" file="slopBed_result2.bed" ftype="bed" />
55 </test>
56 </tests>
35 <help> 57 <help>
36 58 <![CDATA[
37 **What it does** 59 **What it does**
38 60
39 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size). 61 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
40 62
41 .. image:: $PATH_TO_IMAGES/slop-glyph.png 63 .. image:: $PATH_TO_IMAGES/slop-glyph.png
42 64
43 .. class:: warningmark 65 .. class:: warningmark
44 66
45 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. 67 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
46 @REFERENCES@ 68 @REFERENCES@
69 ]]>
47 </help> 70 </help>
48 <expand macro="citations" /> 71 <expand macro="citations" />
49 </tool> 72 </tool>